Deep tunnels and covered trenches have been dropped as alternatives for the Palo Alto/Midpeninsula portion of the state's high-speed-line under the latest plan from the California High Speed Rail Authority, officials disclosed today (Thursday).

The agency dropped the tunnel and cut-and-cover alternatives despite heavy lobbying on their behalf by Palo Alto, Menlo Park, Atherton, Mountain View and other Midpeninsula cities.

A short tunnel under San Francisquito Creek is a possibility, the report indicates -- which would facilitate flood-control planning and possibly remove threats to the root system of the landmark El Palo Alto redwood tree.

The authority board is discussing design options for the San Francisco-to-San Jose segment of the line at its meeting today in San Francisco.

A new staff report lists just two design options for the Peninsula segment: one relies on at-grade and aerial structures and another includes tunnels at several portions of the segment. Tunneling is still an option for a stretch in San Francisco, in the Burlingame/Millbrae area and in Santa Clara, where a major station is planned.

But in Palo Alto, where city leaders and residents have long clamored for an underground tunnel, deep tunnels and covered trenches now appear to be off the table. The only design options recommended by staff engineers are a at-grade trains, aerial viaducts and open trenches, according to a staff summary made public at the meeting.

According to the Supplemental Alternative Analysis, the covered-trench alternative in the Palo Alto area is "impracticable due to major constructability issues" and presents significant ventilation and life safety problems.

A deep tunnel would "result in critical risks due to ground conditions, have major constructability issues, lengthy construction schedule and substantial cost features," the report said.

"Partially or completely covered trench or short-tunnel sections may be constructed to ameliorate either narrow right of way or environmental concerns" on the Peninsula segment, the report states.

"The San Francisquito Creek in Palo Alto could be a location where a short tunnel underneath the creek would be necessary in order to not interfere with the creek's water flow," it states.

It says that in other sections, trenching would be designed "to not preclude future decking or coverage.

"This would allow cities to cover sections of the trench if they found it desirable and if it were acceptable by Caltrain and the Authority."

Covered sections of less than 600 feet could be added later "without requiring sophisticated fire/life safety systems," it said.